Molecular Pathology

The Molecular Pathology Laboratory offers molecular diagnostic testing for a variety of clinical indications across the health-care continuum, including testing for disease susceptibility, population screening, diagnosis, prognosis, therapeutic decision making, and disease monitoring. The test menu has many applications in the areas of hereditary diseases, neoplastic diseases, infectious diseases, and for identity testing. The laboratory uses a spectrum of molecular techniques and platforms to evaluate nucleic acids isolated from patient samples, including real-time PCR, capillary electrophoresis, and pyrosequencing.

The Molecular Pathology Laboratory works closely with other laboratories in the Division of Precision and Computational Diagnostics, including the Center for Personalized Diagnostics and the Cytogenetics Laboratory, to provide integrated and cutting-edge precision molecular and genomic diagnostic services to patients. All faculty members are Board-Certified in Pathology, Clinical Molecular Genetics, and/or Molecular Genetic Pathology.

Notable areas of expertise, summarized below, include molecular genetic testing, identity testing, molecular virology, and molecular profiling of common liquid and solid tumors. Please refer to requisition form [PDF] for full test menu and the online Lab Service Test Guide for specific test details and requirements.


In the News


Testing Highlights

• UPDATE! Testing for Factor II (Prothrombin) and Factor V assay methodology has changed to the Cepheid GeneXpert platform. This is a qualitative, sample to result assay integrating sample purification, nucleic acid amplification, and detection of the target sequence from whole blood using real-time PCR. MTHFR is not detected by this assay.  For more information, please see the laboratory test services guide.

• UPDATE!  The PML/RARA gene fusion assay methodology has been changed to a real-time PCR methodology.  This new assay is similar to the previous assay and will have streamlined reports for new acute leukemia patients that also require RUNX/RUNX1T1 and CBFB/MYH11 testing.  Stand-alone PML/RARA testing will still be available.

• UPDATE! Two new FDA-approved methods for detection of isocirtrate dehydrogenase-1 (IDH) and IDH2 gene variants are now available. These new methods utilize Abbott RealTime PCR to detect 5 single nucleotide variants (SNV) in IDH1 and 9 SNVs in IDH2 in blood and bone marrow specimens. These assays are able to accurately detect variants in specimens with ≥2% variant allele frequency. For more information, please see the laboratory test services guide.

• UPDATE! BCR-ABL1 Quantitative p190 testing is now available in-house. The QuantideX qPCR BCR-ABL minor (p190) assay is similar to the quantitative p210 QuantideX methodology. Results will be reported at a % Ratio of BCR-ABL1 /ABL1 copies/qPCR. The new method has an analytical sensitivity of at least 1:100,000 normal cells with a linear reportable range of 25% Ratio to 0.0036% Ratio.

• UPDATE!  Testing for the CAG repeat expansion in HTT, associated with Huntington Disease, is now available. This assay utilizes a repeat primed PCR followed by capillary electrophoresis to detect CAG repeats and is able to accurately detect expansions of up to 200 CAG repeats. Clinical testing of patients with symptoms (i.e. diagnostic testing) of Huntington Disease and well as testing on those who are asymptomic (i.e predictive testing) or prodromal can be performed using this method. For more information, please see the laboratory test services guide.


Molecular Genetic Testing

• Details about molecular genetic tests are available through the Genetic Test Registry.


Identity Testing

• Chimerism analysis, performed using short tandem repeat PCR, supports the active bone marrow transplant service in the UPenn Health System. The laboratory has 20 years of experience with the technical and analytical aspects of chimerism analysis, including for reduced-intensity and cord blood transplants. Cellular subset analysis is performed for CD3+ and CD33/CD66b+ subset samples.
• Additional applications of identity testing which are available include maternal cell contamination, assessment of graft-versus-host disease, assessment of recipient versus donor origin of tumor, hydatidiform molar evaluation, and sample identification.


Molecular Oncology Testing

• Comprehensive qualitative and quantitative molecular oncology testing is available for diagnosis, disease monitoring, and therapeutic decision making.
• A variety of assays, including MGMT methylation analysis by pyrosequencing and BCR-ABL quantitative PCR, are offered to detect common genetic alterations in solid and hematologic malignancies.
• The Molecular Pathology Laboratory works in conjunction with the Center for Personalized Diagnostics for the testing of molecular oncology specimens. Please inquire with the laboratory for questions or additional information.


Molecular Virology Testing

• Molecular testing is performed for the identification of specific viral infections, including common respiratory pathogens such as influenza A/B and respiratory syncytial virus.
• For selected viruses, quantitative assessment of viral infections as well as monitoring of viral loads is offered in the laboratory.
• Genotyping of hepatitis C and human papillomavirus is also available.
• Sample types acceptable for molecular virology testing depend on the assay requested.



The one-year ACGME-accredited Molecular Genetic Pathology (MGP) fellowship program trains fellows in the practice of molecular pathology and genomics, the application and interpretation of molecular laboratory techniques, and diagnostic laboratory administration. Over the course of the one-year ACGME accredited fellowship the fellow gains experience in the application of molecular pathology through service work, didactic lectures, resident teaching, involvement in laboratory administration, hands-on test development and/or research projects, as well as rotations in cytogenetics, genomics, HLA, virology, biochemical genetics, and clinical adult and pediatric genetics.

find a Specialist
Molecular Pathology
Jennifer J.D. Morrissette, PhD

Associate Professor of Clinical Pathology and Laboratory Medicine

Clinical Director, Center for Personalized Diagnostics

University of Pennsylvania Perelman School of Medicine

Warren S. Pear, MD, PhD

Gaylord P. and Mary Louise Harnwell Professor

Perelman School of Medicine at the University of Pennsylvania

Director, Experimental Pathology and Immunobiology Division

Vivianna Maia Van Deerlin, MD, PhD

Professor of Pathology and Laboratory Medicine at the Hospital of the University of Pennsylvania

University of Pennsylvania Perelman School of Medicine

Christopher D. Watt, MD, PhD

Associate Professor of Clinical Pathology and Laboratory Medicine

Program Director, Molecular Genetic Pathology Fellowship

Associate Director, Molecular Pathology Laboratory

University of Pennsylvania Perelman School of Medicine

Jacquelyn Roth, PhD, DABMGG

Assistant Professor of Clinical Pathology and Laboratory Medicine
Perelman School of Medicine at the University of Pennsylvania